LAMMPS (12 Jun 2025 - Development - patch_12Jun2025-739-g2644e7f6fa-modified)
  using 1 OpenMP thread(s) per MPI task
# Solvated 5-mer peptide

units		real
atom_style	full

pair_style	lj/charmm/coul/long 8.0 10.0 10.0
bond_style      harmonic
angle_style     charmm
dihedral_style  charmm
improper_style  harmonic
kspace_style	pppm 0.0001

read_data	data.peptide
Reading data file ...
  orthogonal box = (36.840194 41.013691 29.768095) to (64.21156 68.385058 57.139462)
  1 by 2 by 2 MPI processor grid
  reading atoms ...
  2004 atoms
  reading velocities ...
  2004 velocities
  scanning bonds ...
  3 = max bonds/atom
  scanning angles ...
  6 = max angles/atom
  scanning dihedrals ...
  14 = max dihedrals/atom
  scanning impropers ...
  1 = max impropers/atom
  orthogonal box = (36.840194 41.013691 29.768095) to (64.21156 68.385058 57.139462)
  1 by 2 by 2 MPI processor grid
  reading bonds ...
  1365 bonds
  reading angles ...
  786 angles
  reading dihedrals ...
  207 dihedrals
  reading impropers ...
  12 impropers
Finding 1-2 1-3 1-4 neighbors ...
  special bond factors lj:    0        0        0       
  special bond factors coul:  0        0        0       
     4 = max # of 1-2 neighbors
     7 = max # of 1-3 neighbors
    14 = max # of 1-4 neighbors
    18 = max # of special neighbors
  special bonds CPU = 0.000 seconds
  read_data CPU = 0.011 seconds

neighbor	2.0 bin
neigh_modify	delay 5

timestep	2.0

group		peptide type <= 12
84 atoms in group peptide
group		one id 2 4 5 6
4 atoms in group one
group		two id 80 82 83 84
4 atoms in group two
group		ref id 37
1 atoms in group ref
group		colvar union one two ref
9 atoms in group colvar

fix		1 all nvt temp 275.0 275.0 100.0 tchain 1

fix		3a one spring couple ref 100.0 0.0 0.0 0.0 10.0
fix		3b two spring couple ref 100.0 0.0 0.0 0.0 10.0

fix		2a ref setforce 0.0 0.0 0.0

fix		4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
Finding SHAKE clusters ...
      19 = # of size 2 clusters
       6 = # of size 3 clusters
       3 = # of size 4 clusters
     640 = # of frozen angles
  find clusters CPU = 0.000 seconds

#dump		1 colvar custom 1 dump.spring.lammpstrj id xu yu zu fx fy fz
#dump_modify 1  sort id

variable sp equal f_3a+f_3b

thermo_style	custom step temp etotal pe ke epair ebond v_sp
thermo		10


run		100
PPPM initialization ...
  using 12-bit tables for long-range coulomb
  G vector (1/distance) = 0.26872465
  grid = 15 15 15
  stencil order = 5
  estimated absolute RMS force accuracy = 0.022820853
  estimated relative force accuracy = 6.872432e-05
  using double precision FFTW3
  3d grid and FFT values/proc = 4312 960
Generated 91 of 91 mixed pair_coeff terms from arithmetic mixing rule
Neighbor list info ...
  update: every = 1 steps, delay = 5 steps, check = yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 12
  ghost atom cutoff = 12
  binsize = 6, bins = 5 5 5
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair lj/charmm/coul/long, perpetual
      attributes: half, newton on
      pair build: half/bin/newton
      stencil: half/bin/3d
      bin: standard
SHAKE stats (type/ave/delta/count) on step 0
Bond:    4   1.111     1.44264e-05        9
Bond:    6   0.996998  7.26967e-06        6
Bond:    8   1.08      1.32536e-05        7
Bond:   10   1.111     1.22749e-05        8
Bond:   12   1.08      1.11767e-05        9
Bond:   14   0.96      0                  1
Bond:   18   0.957206  4.37979e-05     1280
Angle:  31   104.519   0.00396029       640
Per MPI rank memory allocation (min/avg/max) = 16.01 | 16.22 | 16.41 Mbytes
   Step          Temp          TotEng         PotEng         KinEng         E_pair         E_bond          v_sp     
         0   282.10052     -5237.458      -6372.3765      1134.9186     -6442.7679      16.557152      292.14604    
        10   305.06149     -5058.8971     -6286.1899      1227.2929     -6413.1019      58.8499        103.38345    
        20   311.00516     -4999.0612     -6250.266       1251.2048     -6417.1021      47.695297      36.699695    
        30   314.22337     -4993.7011     -6257.8532      1264.152      -6421.9678      35.344144      10.563932    
        40   297.87492     -5020.8375     -6219.2181      1198.3806     -6389.8526      27.723134      3.8354514    
        50   304.0207      -5056.2575     -6279.3632      1223.1057     -6456.8213      55.459507      0.20678213   
        60   285.92576     -5104.0461     -6254.354       1150.3079     -6435.5813      32.76723       0.69352954   
        70   277.83519     -5163.9756     -6281.7343      1117.7587     -6447.7031      39.627168      11.433604    
        80   267.51495     -5206.4046     -6282.644       1076.2394     -6456.6368      31.611883      6.355418     
        90   278.15579     -5245.3824     -6364.431       1119.0485     -6499.8063      28.849773      0.36941574   
SHAKE stats (type/ave/delta/count) on step 100
Bond:    4   1.11098   8.97155e-05        9
Bond:    6   0.996996  1.00568e-05        6
Bond:    8   1.08      6.02345e-06        7
Bond:   10   1.111     1.84253e-05        8
Bond:   12   1.08      7.2713e-06         9
Bond:   14   0.959996  0                  1
Bond:   18   0.957198  3.36079e-05     1280
Angle:  31   104.52    0.0030599        640
       100   260.10611     -5292.6885     -6339.1214      1046.4329     -6471.6733      25.362042      0.2198733    
Loop time of 0.242002 on 4 procs for 100 steps with 2004 atoms

Performance: 71.404 ns/day, 0.336 hours/ns, 413.219 timesteps/s, 828.091 katom-step/s
99.6% CPU use with 4 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.17607    | 0.17921    | 0.18249    |   0.7 | 74.05
Bond    | 0.00019535 | 0.00047629 | 0.0007549  |   0.0 |  0.20
Kspace  | 0.015245   | 0.018842   | 0.021843   |   2.2 |  7.79
Neigh   | 0.03136    | 0.03142    | 0.031463   |   0.0 | 12.98
Comm    | 0.005918   | 0.0060435  | 0.0061393  |   0.1 |  2.50
Output  | 0.00012756 | 0.00014883 | 0.00020829 |   0.0 |  0.06
Modify  | 0.0053922  | 0.0054194  | 0.0054482  |   0.0 |  2.24
Other   |            | 0.0004376  |            |       |  0.18

Nlocal:            501 ave         513 max         489 min
Histogram: 1 0 0 0 1 1 0 0 0 1
Nghost:        6563.25 ave        6596 max        6519 min
Histogram: 1 0 1 0 0 0 0 0 0 2
Neighs:         177059 ave      181742 max      172942 min
Histogram: 1 0 1 0 0 0 1 0 0 1

Total # of neighbors = 708237
Ave neighs/atom = 353.41168
Ave special neighs/atom = 2.3403194
Neighbor list builds = 12
Dangerous builds = 2
Total wall time: 0:00:00
